regexThu, 16 Feb 2023
check an ip or an ftp in one regex for python
^(?:(?:25[0-5]|2[0-4][0-9]|[01]?[0-9][0-9]?)\.){3}(?:25[0-5]|2[0-4][0-9]|[01]?[0-9][0-9]?)$
Arnau Albert Sanchez
All generations.
generate functionWed, 22 Feb 2023
functions to get info from wikipedia API
import wikipedia
def get_info(query):
return wikipedia.summary(query, sentences = 2)
get_info('cat')
Python
Viewtime complexityThu, 16 Feb 2023
def count_files(path): file_list = glob.glob(path) num_of_files = len(file_list) return num_of_files def get_xml_from_ncbi(terms): for i in terms: utils.request_search(db='nucleotide',term=i,retmax=1,xml_filename=f'/bio/practica_2/data/{i}.xml')
O(n)
linuxWed, 15 Mar 2023
put a static ip
sudo vi /etc/network/interfaces
auto lo
iface lo inet loopback
auto eth0
iface eth0 inet static
address 192.168.1.110
netmask 255.255.255.0
gateway 192.168.1.1
dns-nameservers 8.8.4.4 8.8.8.8
linuxSat, 18 Feb 2023
shutdown inmediatly
shutdown -h now #now means inmediatly
regexMon, 06 Mar 2023
if contains R1
^.*R1\b.*$
time complexityThu, 16 Feb 2023
def count_files(path): file_list = glob.glob(path) num_of_files = len(file_list) return num_of_files def get_xml_from_ncbi(terms): for i in terms: utils.request_search(db='nucleotide',term=i,retmax=1,xml_filename=f'/bio/practica_2/data/{i}.xml') def get_files_in_dir(directory_path): directory_path = Path(directory_path) files = [] for file in directory_path.glob('*'): if file.is_file(): files.append(str(file)) return files def get_id_list(list_of_files): id_list = [] for file in list_of_files: dict = utils.read_xml(file) id_for_list = dict['IdList'][0] id_list.append(id_for_list) return id_list def get_gb_files(list_of_id): for id in list_of_id: utils.request_fetch('nucleotide',id,'gb',f'/bio/practica_2/gb_files/{id}.gb') def rename_files_gb(list_of_gb): for file in list_of_gb: record_iter: GenBankIterator = SeqIO.parse(file, 'gb') for record in record_iter: if record.features: for feature in record.features: if feature.type == "source": name_list = feature.qualifiers["organism"] name = name_list[0] reg_white_space = r'\s' pat_white_space = re.compile(reg_white_space) name = pat_white_space.sub('_', name) reg_name = r'\/([^\/]+)$' pat_name = re.compile(reg_name) file_name = pat_name.search(file).group(1) new_file_name = os.path.dirname(file) + '/' + name + os.path.splitext(file_name)[1] os.rename(file, new_file_name)
O(n)
linuxMon, 20 Feb 2023
apt-get auto-remove && apt-get clean && apt-get update && apt-get upgrade
apt-get autoremove && apt-get clean && apt-get update && apt-get upgrade
class from descriptionThu, 16 Feb 2023
create an animal
function Animal(name, type){
this.name = name;
this.type = type;
}
var dog = new Animal("Dog", "Mammal");
var platypus = new Animal("Platypus", "Mammal");
console.log(dog.name, dog.type);
console.log(platypus.name, platypus.type);
Javascript
ViewregexThu, 16 Feb 2023
check an ip or an ftp
/ftp:\/\/\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}/
/\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}/
regexThu, 16 Feb 2023
check an ip or an ftp in one regex
/\d{3}[.-]\d{3}[.-]\d{3}[.-]\d{3}|ftp[.-]\d{3}[.-]\d{3}[.-]\d{3}[.-]\d{3}/
time complexityThu, 16 Feb 2023
import json from pprint import pp from pathlib import Path from Bio import Entrez from typing import Union import re import os import glob import utils from Bio.Entrez.Parser import DictionaryElement, ListElement import utils from Bio import SeqIO from Bio.SeqRecord import SeqRecord from Bio.Entrez.Parser import DictionaryElement, ListElement from Bio.SeqIO.InsdcIO import GenBankIterator Entrez.email = 'carde602@gmail.com' CACHE_DIR = Path('/bio/practica_2/data') from pathlib import Path def count_files(path): file_list = glob.glob(path) num_of_files = len(file_list) return num_of_files def get_xml_from_ncbi(terms): for i in terms: utils.request_search(db='nucleotide',term=i,retmax=1,xml_filename=f'/bio/practica_2/data/{i}.xml') def get_files_in_dir(directory_path): directory_path = Path(directory_path) files = [] for file in directory_path.glob('*'): if file.is_file(): files.append(str(file)) return files def get_id_list(list_of_files): id_list = [] for file in list_of_files: dict = utils.read_xml(file) id_for_list = dict['IdList'][0] id_list.append(id_for_list) return id_list def get_gb_files(list_of_id): for id in list_of_id: utils.request_fetch('nucleotide',id,'gb',f'/bio/practica_2/gb_files/{id}.gb') def rename_files_gb(list_of_gb): for file in list_of_gb: record_iter: GenBankIterator = SeqIO.parse(file, 'gb') for record in record_iter: if record.features: for feature in record.features: if feature.type == "source": name_list = feature.qualifiers["organism"] name = name_list[0] reg_white_space = r'\s' pat_white_space = re.compile(reg_white_space) name = pat_white_space.sub('_', name) reg_name = r'\/([^\/]+)$' pat_name = re.compile(reg_name) file_name = pat_name.search(file).group(1) new_file_name = os.path.dirname(file) + '/' + name + os.path.splitext(file_name)[1] os.rename(file, new_file_name) # def rename_files(directory_path): # list_of_files = get_files_in_dir(directory_path) # list_of_parser_files = [] # for file in list_of_files: # file_parsed:GenBankIterator = SeqIO.parse(file,'gb') # list_of_parser_files.append(file_parsed) # return list_of_parser_files # Main # --------------------------------------------------------------------- this_module: str = __name__ main_module: str = "__main__" if this_module == main_module: # List of term to search for the id list_of_terms = ['Rabies lyssavirus isolate 18018LIB, complete genome','ebolavirus, complete genome','Marburg marburgvirus isolate MARV001, complete genome','Nipah virus, complete genome','Variola virus[ORGN]', 'TREPONEMA PALLIDUM TRIPLET ','Method of Immunization against the 4 serotypes of Dengue fever','Kyasanur forest disease virus isolate W6204 NS5 gene, partial cds'] data_to_count = '/bio/practica_2/data/*' gb_files_to_count = 'practica_2/gb_files/*' data = '/bio/practica_2/data' gb_files = 'practica_2/gb_files' num_of_xml_files_before_search_in_ncbi = count_files(data_to_count) num_of_gb_files_before_search_in_ncbi = count_files(gb_files_to_count) # Get the xml from ncbi print(num_of_xml_files_before_search_in_ncbi) print(num_of_gb_files_before_search_in_ncbi) if num_of_xml_files_before_search_in_ncbi == 0: get_xml_from_ncbi(list_of_terms) print('excecuted: get_xml_from_ncbi') if num_of_xml_files_before_search_in_ncbi > 0: list_of_xml = get_files_in_dir(data) id_list = get_id_list(list_of_xml) print(id_list) get_gb_files(id_list) print('excecuted: get_gb_files') if num_of_gb_files_before_search_in_ncbi > 0: list_of_gb = get_files_in_dir(gb_files) rename_files_gb(list_of_gb) print('excecuted: rename_files_gb')
O(n)
linuxMon, 20 Feb 2023
autoremove + clean + update + upgrade in the same command
sudo apt autoremove && sudo apt clean && sudo apt update && sudo apt upgrade
generate functionThu, 16 Feb 2023
create a fasta file with a random sequence
function() {
var seq = '';
for (var i=0; i < 100; i++) {
seq += 'ACGT'.charAt(Math.floor(Math.random()*4));
}
return '>seq1\n'+seq;
}
Javascript
Viewgenerate functionWed, 22 Feb 2023
functions to get info from wikipedia
import wikipedia
wikipedia.search("John") # => ['John', 'John (artist)', 'John the Baptist', 'John (given name)', 'John the Revelator', 'John Doe', 'John Lennon', 'John Smith', 'John of Gaunt', 'John Mayall']
wikipedia.summary("John", sentences=1) # => 'John is a common English name and surname: John (given name) John (surname), including a list of people with the name John'
wikipedia.suggest("John") # => 'John'
Python
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